Help:Tutorial:Step 3 v2

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This step explains how to add cellular compartment information, how to illustrate intercellular transport, use of labels, copy and paste, creating and connecting complexes and adding a literature reference.
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[[:Help:Tutorial:Step_4_v2|Next step]] | [[:Help:Tutorial|Index]]
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All the steps are visually represented in the below video.
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[[:Help:Tutorial:Step_4_v2|Next step]] | [[:Help:Tutorial|Index]]
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{{#ev:youtube|A_ZWFXjtpNQ|700|left|Create pathway, part1}}
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= Completing the pathway =
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This step explains how to add cellular compartment information, illustrating transport out of the cell, use of labels, copy and paste, creating and connecting complexes and adding a literature reference.
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<!-- Uncomment after mediawiki upgrade
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{{#ev:youtube|A_ZWFXjtpNQ|700|left|Create pathway, part1}}-->
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This tutorial starts with a few more entities added to the Demo pathway. You can either add the remaining entities manually, or start with the [[:Pathway:WP3539|Demo_part3]] pathway.
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This tutorial starts with a few more entities added to the Demo pathway.  
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Starting with the ''Demo_part3'' pathway, we have all the intracellular components of the pathway. The next steps include adding a cellular compartment, and illustrating the translocation of Cholesterol out of the cell. First, open the editor and start full-screen mode.
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==  Add a cellular compartment ==
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==  Adding a cellular compartment ==
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* To add a cellular compartment shape to the pathway, select the ''Cell'' shape from the right-side ''Objects'' panel and place it on the drawing board.  
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* To add a cellular compartment shape to the pathway, select the '''Cell''' shape [[image:CellShape.png|30px]] from the right-side '''Objects''' panel and place it on the drawing board.  
* Size and position the cell shape to fit all the pathway entities. The cell shape should be a large rectangle.
* Size and position the cell shape to fit all the pathway entities. The cell shape should be a large rectangle.
== Adding labels ==
== Adding labels ==
When using cellular compartments in a pathway, add labels for clarity:
When using cellular compartments in a pathway, add labels for clarity:
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* In the toolbar, select the ''Label'' objects and place it at the bottom right corner of the cell shape.
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* In the toolbar, click the '''Label''' button {{TutorialImage|newlabel.gif}} and place it at the bottom right corner of the cell shape.
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* Double-click the label to open the ''Label properties'' interface, and type in ''Liver cell''. In this interface you can also change the font style and size of the label.
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* Double-click the label to open the '''Label properties''' interface, and type in "Liver cell". In this interface you can also change the font style and size of the label.
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* Repeat these steps to add another label just outside the cell shape, for ''Plasma''.
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* Repeat these steps to add another label just outside the cell shape, for '''Plasma'''.
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== Illustrating intercellular transport ==
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Label text and style can also be edited in the '''Properties''' tab of the right-side panel.
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== Illustrating transport ==
To illustrate the transport of cholesterol out of the liver cell, we place a copy of the cholesterol node in the area representing plasma:
To illustrate the transport of cholesterol out of the liver cell, we place a copy of the cholesterol node in the area representing plasma:
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* Select the cholesterol node, and click the ''Copy selected pathway objects to clipboard'' button in the toolbar.
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* Select the cholesterol node, and click the '''Copy selected pathway objects to clipboard''' button {{TutorialImage|copy.gif}} in the toolbar.
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* Next, click the ''Paste pathway objects from clipboard'' button. This creates a new copy of the cholesterol node.
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* Next, click the '''Paste pathway objects from clipboard''' button {{TutorialImage|paste.gif}}. This creates a new copy of the cholesterol node.
* Place the copy of the node outside the liver cell, under the original copy of the cholesterol node.
* Place the copy of the node outside the liver cell, under the original copy of the cholesterol node.
== Creating and connecting complexes ==
== Creating and connecting complexes ==
The transport of cholesterol out of the liver cell is facilitated by a transfer protein complex, composed of MTTP and PDIA2.  
The transport of cholesterol out of the liver cell is facilitated by a transfer protein complex, composed of MTTP and PDIA2.  
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* Add two new GeneProduct data nodes and annotate them as ''PDIA2'' and ''MTTP''.  
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* Add two new GeneProduct data nodes and annotate them as "PDIA2" and "MTTP".  
* Select both nodes either by Command+Click or click and drag.
* Select both nodes either by Command+Click or click and drag.
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* In the toolbar, click the ''Stack vertical center'' button {{TutorialImage|stackverticalcenter.gif}} to stack the nodes.
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* In the toolbar, click the '''Stack vertical center''' button {{TutorialImage|stackverticalcenter.gif}} to stack the nodes.
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* To create a complex, first select the two nodes again and then right-click and select ''Create complex''.
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* To create a complex, first select the two nodes again and then right-click and select '''Create complex''', or clicking '''Ctrl-P'''.
* Place the complex in the plasma membrane, under SOAT1.
* Place the complex in the plasma membrane, under SOAT1.
Next, we can illustrate the transfer of cholesterol by adding an interaction:
Next, we can illustrate the transfer of cholesterol by adding an interaction:
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* Add an interaction of type ''MIM conversion'' and connect it to go from the intracellular cholesterol node to the extracellular cholesterol node.
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* Add an interaction of type '''MIM conversion''' and connect it to go from the intracellular cholesterol node to the extracellular cholesterol node.
* Next, add an anchor to the interaction.
* Next, add an anchor to the interaction.
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* Add a new interaction of type ''MIM catalysis''.
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* Add a new interaction of type '''MIM catalysis'''.
* Connect the catalysis interaction from the MTTP/PDIA2 complex to the anchor on the transfer interaction.
* Connect the catalysis interaction from the MTTP/PDIA2 complex to the anchor on the transfer interaction.
* Finally, move the complex to the right so that it is placed in the plasma membrane on the cholesterol transfer interaction.
* Finally, move the complex to the right so that it is placed in the plasma membrane on the cholesterol transfer interaction.
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Since we have a literature reference describing how MTTP/PDIA2 facilitates cholesterol transfer, we can add it to the MTTP/PDIA2 complex:
Since we have a literature reference describing how MTTP/PDIA2 facilitates cholesterol transfer, we can add it to the MTTP/PDIA2 complex:
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* To add a literature reference to the complex, right-click on the complex and select ''Literature > Add literature reference''.  
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* To add a literature reference to the complex, right-click on the complex and select '''Literature > Add literature reference'''.  
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* In the ''Literature reference properties'' type in the PMID for the reference and click ''Search''. When the PMID is found, the fields are completed.
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* In the '''Literature reference properties''' type in the PMID for the reference and click '''Search'''. When the PMID is found, the fields are completed. You can also manually fill in the reference information manually as well.
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* Double-check that the correct reference was found, then click ''OK''.
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* Double-check that the correct reference was found, then click '''OK'''.
* Save your pathway to WikiPathways, and enter a description for your changes when prompted.  
* Save your pathway to WikiPathways, and enter a description for your changes when prompted.  
* Exit full-screen mode and close the editor.
* Exit full-screen mode and close the editor.
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{{Template:TutorialHint|You can add references to any individual element or groups. You can also add a general reference at the pathway level by right-clicking the pathway infobox and selecting '''Literature > Add literature reference'''}}
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== Saving changes ==
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*  To save the pathway, go to '''Plugins -> WikiPathways -> Update'''. You will be asked to provide a description of your changes.
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*  Once the pathway is saved at WikiPathways, the Pathway Page will be updated with your changes.
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[[:Help:Tutorial:Step_4_v2|Next step]] | [[:Help:Tutorial|Index]]

Current revision


Next step | Index Next step | Index

Completing the pathway

This step explains how to add cellular compartment information, illustrating transport out of the cell, use of labels, copy and paste, creating and connecting complexes and adding a literature reference.

This tutorial starts with a few more entities added to the Demo pathway.

Adding a cellular compartment

  • To add a cellular compartment shape to the pathway, select the Cell shape from the right-side Objects panel and place it on the drawing board.
  • Size and position the cell shape to fit all the pathway entities. The cell shape should be a large rectangle.

Adding labels

When using cellular compartments in a pathway, add labels for clarity:

  • In the toolbar, click the Label button newlabel.gif and place it at the bottom right corner of the cell shape.
  • Double-click the label to open the Label properties interface, and type in "Liver cell". In this interface you can also change the font style and size of the label.
  • Repeat these steps to add another label just outside the cell shape, for Plasma.

Label text and style can also be edited in the Properties tab of the right-side panel.

Illustrating transport

To illustrate the transport of cholesterol out of the liver cell, we place a copy of the cholesterol node in the area representing plasma:

  • Select the cholesterol node, and click the Copy selected pathway objects to clipboard button copy.gif in the toolbar.
  • Next, click the Paste pathway objects from clipboard button paste.gif. This creates a new copy of the cholesterol node.
  • Place the copy of the node outside the liver cell, under the original copy of the cholesterol node.

Creating and connecting complexes

The transport of cholesterol out of the liver cell is facilitated by a transfer protein complex, composed of MTTP and PDIA2.

  • Add two new GeneProduct data nodes and annotate them as "PDIA2" and "MTTP".
  • Select both nodes either by Command+Click or click and drag.
  • In the toolbar, click the Stack vertical center button stackverticalcenter.gif to stack the nodes.
  • To create a complex, first select the two nodes again and then right-click and select Create complex, or clicking Ctrl-P.
  • Place the complex in the plasma membrane, under SOAT1.

Next, we can illustrate the transfer of cholesterol by adding an interaction:

  • Add an interaction of type MIM conversion and connect it to go from the intracellular cholesterol node to the extracellular cholesterol node.
  • Next, add an anchor to the interaction.
  • Add a new interaction of type MIM catalysis.
  • Connect the catalysis interaction from the MTTP/PDIA2 complex to the anchor on the transfer interaction.
  • Finally, move the complex to the right so that it is placed in the plasma membrane on the cholesterol transfer interaction.

Adding a literature reference

Since we have a literature reference describing how MTTP/PDIA2 facilitates cholesterol transfer, we can add it to the MTTP/PDIA2 complex:

  • To add a literature reference to the complex, right-click on the complex and select Literature > Add literature reference.
  • In the Literature reference properties type in the PMID for the reference and click Search. When the PMID is found, the fields are completed. You can also manually fill in the reference information manually as well.
  • Double-check that the correct reference was found, then click OK.
  • Save your pathway to WikiPathways, and enter a description for your changes when prompted.
  • Exit full-screen mode and close the editor.

Note: You can add references to any individual element or groups. You can also add a general reference at the pathway level by right-clicking the pathway infobox and selecting Literature > Add literature reference

Saving changes

  • To save the pathway, go to Plugins -> WikiPathways -> Update. You will be asked to provide a description of your changes.
  • Once the pathway is saved at WikiPathways, the Pathway Page will be updated with your changes.

Next step | Index

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